README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# motif <img src="man/figures/logo.png" align="right" width="150" />

<!-- badges: start -->
[![CRAN status](http://www.r-pkg.org/badges/version/motif)](https://cran.r-project.org/package=motif)
[![GitHub action build status](https://github.com/Nowosad/motif/workflows/pkgdown/badge.svg)](https://github.com/Nowosad/motif/actions)
[![Codecov test coverage](https://codecov.io/gh/Nowosad/motif/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Nowosad/motif?branch=master)
[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/motif)](https://cran.r-project.org/package=motif)
<!-- badges: end -->

The **motif** package implements and extends ideas of the pattern-based spatial analysis in R.
It describes spatial patterns of categorical raster data for any defined regular and irregular areas. 
Patterns are represented quantitatively using built-in signatures based on co-occurrence matrices but also allows for any user-defined functions. 
It enables spatial analysis such as search, change detection, and clustering to be performed on spatial patterns.

## Installation

You can install the released version of motif from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("motif")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("Nowosad/motif")
```

## Documentation

See the package's vignettes:

1. [Introduction to the motif package](https://jakubnowosad.com/motif/articles/v1_intro.html)
2. [Types of spatial patterns' signatures](https://jakubnowosad.com/motif/articles/v2_signatures.html)
3. [Spatial patterns' search](https://jakubnowosad.com/motif/articles/v3_search.html)
4. [Spatial patterns' comparision](https://jakubnowosad.com/motif/articles/v4_compare.html)
5. [Spatial patterns' clustering](https://jakubnowosad.com/motif/articles/v5_cluster.html)
6. [Extracting the proportion of different classes in many regular local landscapes](https://jakubnowosad.com/motif/articles/v6_composition.html)

## Contribution

Contributions to this package are welcome.
The preferred method of contribution is through a GitHub pull request. 
Feel free to contact us by creating [an issue](https://github.com/Nowosad/motif/issues). 

## Citation

To cite the `motif` package in publications, please use [this paper](https://doi.org/10.1007/s10980-020-01135-0):

Nowosad, J. Motif: an open-source R tool for pattern-based spatial analysis. Landscape Ecol (2021). https://doi.org/10.1007/s10980-020-01135-0

LaTeX/BibTeX version can be obtained with:
```
library(motif)
citation("motif")
```